The government is running the risk of making it more difficult to convict rapists by relaxing the rules for retaining the DNA of suspects, the shadow home secretary Yvette Cooper has warned.

Parliament is due to debate the government's protection of freedoms bill on Tuesday, which includes plans to limit the retention of DNA to three years in England and Wales. Labour, which says DNA should be retained for six years, says the government's plan would lead to 1,500 fewer detections per year.

Cooper is alarmed that DNA will be retained only in "limited circumstances" if someone is arrested but not charged with rape. Labour said this was a "huge missed opportunity" because studies have shown that the reoffending rate for rape is as high as 29%.

The shadow home secretary said: "The government is going too far in restricting the use of DNA from suspects who have been arrested. Rape cases could be particularly affected. There are already far too few rape convictions, but this change will make it even harder – 69% of rape cases involve arrests but never make it to trial.

"In most of those cases, the police will no longer be able to keep the suspect's DNA even for a short period. Yet the evidence shows DNA has played a crucial role in some extremely serious cases, stopping highly dangerous criminals, including serial rapists previously arrested.

"If the government are serious about increasing the rape conviction rate, they should urgently think again."

The Conservatives and the Liberal Democrats declared in their coalition agreement they would "adopt the protections of the Scottish model for the DNA database", which is less stringent than the database that covers England and Wales.

The coalition pledge took on board the Lib Dem manifesto promise to "remove innocent people from the police DNA database and stop storing DNA from innocent people and children in the future" and the Tories' insistence that the "indefinite retention of innocent people's DNA is unacceptable", although they did describe it as a "useful tool for solving crimes".

Labour says the DNA database provides police with about 3,300 matches every month. In 2009, there were 832 positive matches in cases of rape, murder and manslaughter.

Cooper said: "The government is making it harder for the police to solve serious crimes. They are going too far in restricting the use of DNA from suspects who have been arrested. Of course there must be safeguards in the system, but sensible use of DNA also helps catch very dangerous criminals and prevents innocent people being wrongly charged, too.

"The evidence shows that too many serious crimes will go unsolved if they go this far. These restrictions go much further than the sensible changes Alan Johnson drew up before the election and they are getting the balance wrong."